PCNX1

pecanex 1

Basic information

Region (hg38): 14:70907405-71115382

Previous symbols: [ "PCNXL1", "PCNX" ]

Links

ENSG00000100731NCBI:22990OMIM:617655HGNC:19740Uniprot:Q96RV3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PCNX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PCNX1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
5
clinvar
5
clinvar
10
missense
19
clinvar
3
clinvar
4
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
1
clinvar
1
Total 0 0 19 8 10

Variants in PCNX1

This is a list of pathogenic ClinVar variants found in the PCNX1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
14-70907862-G-C not specified Uncertain significance (Nov 16, 2021)2412001
14-70907901-C-T Likely benign (Apr 01, 2022)2644348
14-70946990-G-A not specified Uncertain significance (Sep 01, 2021)2247629
14-70946994-A-C Benign (Oct 09, 2018)714580
14-70947065-C-G Likely benign (Apr 01, 2022)2644349
14-70976988-C-T Likely benign (Apr 30, 2018)718355
14-70977031-T-C Likely benign (Jun 01, 2022)2644350
14-70977098-C-G not specified Uncertain significance (Nov 08, 2021)2350318
14-70977099-T-G Benign (Jan 01, 2023)2644351
14-70977260-G-A not specified Uncertain significance (Nov 15, 2021)2372969
14-70977684-T-C Benign (Jul 04, 2018)716007
14-70977710-C-T not specified Likely benign (Oct 27, 2021)2285840
14-70977749-C-G Benign (Dec 31, 2019)788802
14-70978076-A-G not specified Uncertain significance (Nov 16, 2021)2394841
14-70978120-A-C not specified Uncertain significance (Jun 11, 2021)3210391
14-70978353-G-A Benign (Dec 31, 2019)768660
14-70978354-C-T not specified Uncertain significance (Nov 09, 2021)2260314
14-70978516-G-C not specified Uncertain significance (Nov 12, 2021)2260959
14-70978539-A-G Benign (May 03, 2018)776847
14-70988600-G-A Likely benign (May 18, 2018)787719
14-70988677-T-C Benign (Oct 09, 2018)715050
14-70988692-C-T not specified Uncertain significance (Oct 29, 2021)2258011
14-71009651-C-G not specified Uncertain significance (Jul 27, 2021)2223728
14-71019061-G-T Malignant tumor of prostate Uncertain significance (-)161686
14-71033444-C-G not specified Uncertain significance (Nov 15, 2021)2256508

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PCNX1protein_codingprotein_codingENST00000304743 36207978
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000001391257060421257480.000167
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.4311241.27e+30.8870.000068715288
Missense in Polyphen408579.560.703986918
Synonymous-0.3754744641.020.00002364690
Loss of Function8.35171130.1510.000006741259

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002680.000268
Ashkenazi Jewish0.0004040.000397
East Asian0.0002180.000163
Finnish0.0001400.000139
European (Non-Finnish)0.0001790.000176
Middle Eastern0.0002180.000163
South Asian0.0001630.000163
Other0.000.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
rvis_EVS
-1.95
rvis_percentile_EVS
1.87

Haploinsufficiency Scores

pHI
0.126
hipred
N
hipred_score
0.466
ghis
0.595

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
gene_indispensability_score

Mouse Genome Informatics

Gene name
Pcnx
Phenotype

Gene ontology

Biological process
Cellular component
integral component of membrane
Molecular function